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Tr/add thinning function #113

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347dd06
Add thin NCDataset function
imreddyTeja Feb 26, 2025
c85252c
Update ClimaArtifactsHelper deps in Manifest
imreddyTeja Feb 28, 2025
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1 change: 1 addition & 0 deletions ClimaArtifactsHelper.jl/Project.toml
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Expand Up @@ -6,6 +6,7 @@ version = "0.0.1"
[deps]
ArtifactUtils = "8b73e784-e7d8-4ea5-973d-377fed4e3bce"
Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
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51 changes: 49 additions & 2 deletions ClimaArtifactsHelper.jl/src/ClimaArtifactsHelper.jl
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Expand Up @@ -3,13 +3,13 @@ module ClimaArtifactsHelper
using ArtifactUtils
using REPL.TerminalMenus
using Pkg.Artifacts
using NCDatasets

import SHA: sha1
import Downloads: download

export create_artifact_guided,
create_artifact_guided_one_file,
download_rate_callback
create_artifact_guided_one_file, download_rate_callback, thin_NCDataset!

const MB = 1024 * 1024
const GB = 1024 * MB
Expand Down Expand Up @@ -261,4 +261,51 @@ function create_artifact_guided_one_file(
create_artifact_guided(output_dir; artifact_name, append)
end

"""
thin_NCDataset!(ds_out::NCDataset, ds_in::NCDataset, thinning_factor=6, dims...)

Fills `ds_out` with a thinned version of `ds_in` by a factor of `thinning_factor` in the dimensions `dims`.
If no dimensions are provided, all dimensions are thinned.
"""
function thin_NCDataset!(ds_out::NCDataset, ds_in::NCDataset, thinning_factor = 6, dims...)
# check that requested regrid dimensions are in the dataset.
all(in.(dims, Ref(keys(ds_in.dim)))) || error("Not all of $dims are in the dataset")
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@ph-kev ph-kev Feb 28, 2025

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Why we need a Ref here? Can you add a comment explaining this or find an alternative solution?

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@imreddyTeja imreddyTeja Mar 28, 2025

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Ref prevents broadcasting over the list of dimensions in the input file. I think this is done pretty commonly.

@show typeof(ds_out.attrib)
@show ds_in.attrib
old_history = get(ds_out.attrib, "history", "")
ds_out.attrib["history"] =
old_history * "; Thinned by a factor of $thinning_factor in dimensions $dims"
for (dim_name, dim_length) in ds_in.dim
if dim_name in dims
defDim(ds_out, dim_name, Int(ceil(ds_in.dim[dim_name] // thinning_factor)))
else
defDim(ds_out, dim_name, ds_in.dim[dim_name])
end
end
for (varname, var) in ds_in
var_dims = dimnames(var)
input_indices = map(var_dims) do dim_name
dim_name in dims ? range(1, ds_in.dim[dim_name]; step = thinning_factor) : Colon()
end
defVar(ds_out, varname, var[input_indices...], dimnames(var), attrib = var.attrib)
end
end

"""
thin_NCDataset!(ouput_path, input_path, thinning_factor=6, dims...)

Create and thin a new NetCDF file at `ouput_path` from the file at `input_path` by a factor of
`thinning_factor` in the dimensions `dims`. This method also copies the global attributes.
"""
function thin_NCDataset!(ouput_path, input_path, thinning_factor = 6, dims...)
ds_in = NCDataset(input_path)
ds_out = NCDataset(ouput_path, "c"; attrib = copy(ds_in.attrib))
thin_NCDataset!(ds_out, ds_in, thinning_factor, dims...)
close(ds_out)
close(ds_in)
end

thin_NCDataset!(ds_out::NCDataset, ds_in::NCDataset, thinning_factor = 6) =
thin_NCDataset!(ds_out, ds_in, thinning_factor, keys(ds_in.dim)...)

end
2 changes: 1 addition & 1 deletion aerosol_concentrations/Manifest.toml
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Expand Up @@ -70,7 +70,7 @@ weakdeps = ["SparseArrays"]
ChainRulesCoreSparseArraysExt = "SparseArrays"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion bedrock_depth/Manifest.toml
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Expand Up @@ -46,7 +46,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.3"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion bonan_richards_eqn/Manifest.toml
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Expand Up @@ -28,7 +28,7 @@ uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
version = "0.1.9"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion clm_data/Manifest.toml
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Expand Up @@ -28,7 +28,7 @@ uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
version = "0.1.9"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion co2_dataset/Manifest.toml
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Expand Up @@ -28,7 +28,7 @@ uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
version = "0.1.9"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion era5_cloud/Manifest.toml
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Expand Up @@ -44,7 +44,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.3"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion era5_lai_covers/Manifest.toml
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Expand Up @@ -193,7 +193,7 @@ weakdeps = ["GeoMakie", "Makie"]
ClimaAnalysisMakieExt = "Makie"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion era5_monthly_averages_2008/Manifest.toml
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Expand Up @@ -46,7 +46,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.3"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion era5_monthly_averages_pressure_levels_1979_2024/Manifest.toml
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Expand Up @@ -46,7 +46,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.3"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion era5_monthly_averages_single_level_1979_2024/Manifest.toml
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Expand Up @@ -46,7 +46,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.3"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion forty_yrs_era5_land_forcing_data/Manifest.toml
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Expand Up @@ -46,7 +46,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.3"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion historical_sst_sic/Manifest.toml
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Expand Up @@ -44,7 +44,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.3"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion landsea_mask/Manifest.toml
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Expand Up @@ -100,7 +100,7 @@ uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"
version = "0.2.6"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion lehmann2008_evaporation/Manifest.toml
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Expand Up @@ -26,7 +26,7 @@ uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
version = "0.1.9"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion merra2_AOD/Manifest.toml
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Expand Up @@ -44,7 +44,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.4"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion merra2_aerosols/Manifest.toml
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Expand Up @@ -72,7 +72,7 @@ weakdeps = ["SparseArrays"]
ChainRulesCoreSparseArraysExt = "SparseArrays"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
Expand Down
2 changes: 1 addition & 1 deletion ozone_concentrations/Manifest.toml
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Expand Up @@ -44,7 +44,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.3"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion precipitation_obs/Manifest.toml
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Expand Up @@ -26,7 +26,7 @@ uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
version = "0.1.8"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion radiation_obs/Manifest.toml
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Expand Up @@ -26,7 +26,7 @@ uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
version = "0.1.9"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
Expand Down
2 changes: 1 addition & 1 deletion soil_ic_2008_50m/Manifest.toml
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Expand Up @@ -46,7 +46,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.4"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion surface_temperatures/Manifest.toml
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Expand Up @@ -44,7 +44,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.3"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion sw_albedo/Manifest.toml
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Expand Up @@ -44,7 +44,7 @@ uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.3"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion topo_drag/Manifest.toml
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Expand Up @@ -26,7 +26,7 @@ uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
version = "0.1.9"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
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2 changes: 1 addition & 1 deletion water_conservation_test/Manifest.toml
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Expand Up @@ -28,7 +28,7 @@ uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
version = "0.1.9"

[[deps.ClimaArtifactsHelper]]
deps = ["ArtifactUtils", "Downloads", "Pkg", "REPL", "SHA"]
deps = ["ArtifactUtils", "Downloads", "NCDatasets", "Pkg", "REPL", "SHA"]
path = "../ClimaArtifactsHelper.jl"
uuid = "6ffa2572-8378-4377-82eb-ea11db28b255"
version = "0.0.1"
Expand Down